I'm running Windows 8.1 and had this same problem with the Malware Protection not completely starting. I tried several of the fixes that I have seen on these forums. And what finally worked for my system was to perform the below steps.
1. Remove Malwarebytes using Control Panel: Program and Features. And as noted in this forum make sure you have your license number.
2. Then in Explorer I ran a search looking for Malwarebytes. I then deleted all files and folders associated with Malwarebytes. Be sure you have all files and folders Unhidden. In Windows 8.01 you can do this in Explorer having the C drive highlighted, go to View; And Check the box that says "Hidden Items". Once all files and folders are not Hidden you will see the folder ProgramData; Malwarebytes. But to delete this folder I had to go into Safe Mode to delete all items.
3. After deleting all items I then rebooted into Windows and ran Aces Utilities; Clean System Registry. Or you can use whatever Registry Cleaner you like.
4. Then I ran the file for Malwarebytes Premium 3.0.6.1469 and once finished I went into the program. Under Protection I enabled the "Enable Self-Protection Module Early Start"
5. After completing these steps I then rebooted and when I brought up Malwarebytes all Protection was working including Malware Protection. I have been running this for several days now and it has worked every time even with rebooting several times during a day. I had worked on this for a few days trying to figure out what would work and so far this has worked for my machine.
I'm also running Malwarebytes Adwcleaner, Norton 360 Premier, Emisisoft Anti-Malware, and I was also running Search and Destroy but removed that for now due to problems it was causing with Explorer of which I will work on that problem next. This version of Malwarebytes seams to work well with all of these other protection programs including S&D.
I will continue to keep watch on how this version performs and update this forum if I have any problems.
Hopefully there will be an update soon so that everyone can have a well protected system.